Research workbench
Structure of aIF2-gamma H97A variant from Sulfolobus solfataricus bound to GTP
Analyse Structure of aIF2-gamma H97A variant from Sulfolobus solfataricus bound to GTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4RD1
- Type
- protein
- Length
- 414 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.5
- Source
- Sulfolobus solfataricus
- Molecule
- Translation initiation factor 2 subunit gamma
- UniProt
- Q980A5
- Ligands
- GDP, GTP, MG, PO4
- Pockets
- 5 · best druggability 0.55
Structure
x-ray diffraction · resolution 1.5 · 1 distinct chain · 19% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Translation initiation factor 2 subunit gamma | protein | 414 | 19% helix, 39% strand | Q980A5 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · 2 copies · chains A
- PO4 · Phosphate ion · ion · chains A
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.55 | 0.77 | 34 | empty |
| 2 | 216 | 0.50 | 0.76 | 33 | GDP |
| 3 | 99 | 0.44 | 0.79 | 25 | GTP, GDP, MG, PO4 |
| 4 | 103 | 0.39 | 0.76 | 20 | empty |
| 5 | 61 | 0.28 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4RD1 · Structure of AIF2-gamma H97A variant from sulfolobus solfataricus bound to GTP · the same entry in another collection · chain A against A, TM-score 1.00
- Q980A5 · AlphaFold monomer V2.0 prediction for translation initiation factor 2 subunit gamma… · a predicted model of the same protein · chain A against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q980A5
- Elsewhere: RCSB PDB 4RD1 · PDBe 4RD1 · UniProt Q980A5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.